% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (c) 1992-2001 Regents of the University of California, Santa Cruz % % Sequence Alignment and Modeling Software System % http://www.cse.ucsc.edu/research/compbio/sam.html % % ----------------- Citations (SAM, SAM-T2K, HMMs) -------------------- % R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: % Extension and analysis of the basic method, CABIOS 12:95-107, 1996. % K. Karplus, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % stridefoo.1.YGR032W.t2k-100-30-stride-ebghtl Host: farm08 Wed Nov 17 23:36:10 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR032W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR032W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR032W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 1896 nodes, 2556.60 seconds % % Sequence scores selected if better than: % E-value (Emax 4.0e+01) (select_score=4) % % Simple: NLL-NULL using FIM probabilities % Reverse: NLL-NULL for the reverse sequence NULL model % Calculated when Simple < simple_threshold (0.00) % E-value on N (=10700) sequences: % N / (1 + exp(-(lambda(=1.4697) * Reverse)^tau(=0.7209))) % Calculated when Simple < simple_threshold (0.00) % Rescale E-values or use -dbsize for multiple scoring runs. % Scores sorted by E-value, best first % % Sequence ID Length Simple Reverse E-value X count 1qbkB 890 -54.39 -16.85 4.35e-01 1jb0A 755 -53.47 -15.39 8.23e-01 1cjaA 342 -30.99 -13.95 1.58e+00 1ah7 245 -39.80 -13.69 1.77e+00 1h2vC 771 -53.82 -12.95 2.50e+00 1jipA 403 -35.59 -12.71 2.78e+00 1j0mA 752 -33.05 -12.50 3.08e+00 1iapA 211 -31.36 -12.42 3.19e+00 1eupA 403 -36.81 -11.93 4.03e+00 1so2A 420 -39.93 -11.81 4.27e+00 1ovlA 271 -37.07 -11.34 5.36e+00 1jcqA 382 -37.76 -11.09 6.04e+00 1xis 387 -30.65 -10.93 6.54e+00 2xis 387 -30.63 -10.91 6.61e+00 1h6kA 757 -51.64 -10.84 6.82e+00 3xis 387 -30.42 -10.83 6.84e+00 1eguA 731 -38.95 -10.79 6.99e+00 1keyA 235 -36.02 -10.58 7.76e+00 1lxkA 721 -39.60 -10.55 7.88e+00 1gw9A 388 -30.61 -10.52 7.98e+00 1mnzA 388 -30.68 -10.43 8.34e+00 4xis 387 -30.19 -10.40 8.49e+00 1e8yA 966 -41.80 -10.38 8.55e+00 1ld8A 382 -37.15 -10.35 8.69e+00 1tn6A 382 -37.11 -10.16 9.52e+00 1oxa 403 -33.37 -10.14 9.62e+00 1ca1 370 -36.43 -10.04 1.01e+01 1pv6A 417 -64.05 -10.02 1.02e+01 1dquA 538 -29.53 -10.01 1.03e+01 2bidA 197 -29.91 -9.90 1.09e+01 2pflA 759 -36.41 -9.72 1.19e+01 1mhyB 395 -39.92 -9.51 1.32e+01 1tbfA 347 -36.51 -9.49 1.34e+01 1mhyG 169 -26.41 -9.48 1.34e+01 1pu6A 218 -29.25 -9.33 1.45e+01 1vljA 407 -35.33 -9.25 1.51e+01 1a8b 318 -31.12 -9.19 1.56e+01 1ft1A 377 -36.33 -9.17 1.57e+01 2pgd 482 -36.26 -9.13 1.60e+01 1itcA 516 -28.89 -9.09 1.64e+01 1r8iA 213 -30.93 -9.05 1.68e+01 1gcvA 140 -26.72 -9.03 1.69e+01 1u19A 349 -52.78 -8.99 1.73e+01 2ran 316 -30.74 -8.95 1.76e+01 1b77A 228 -20.41 -8.78 1.92e+01 1t7pA 698 -39.36 -8.77 1.93e+01 1qjbA 245 -33.82 -8.76 1.95e+01 1hzxA 349 -51.91 -8.74 1.97e+01 1ppjC 379 -52.45 -8.72 1.98e+01 1ezfA 340 -43.04 -8.70 2.01e+01 1ak0 270 -28.61 -8.65 2.05e+01 1fkmA 396 -40.43 -8.65 2.06e+01 1dnpA 471 -29.41 -8.53 2.18e+01 1qjaA 245 -35.72 -8.53 2.19e+01 1rmi 160 -29.62 -8.52 2.20e+01 1a8a 318 -29.95 -8.50 2.23e+01 1n7oA 721 -38.27 -8.46 2.27e+01 1d8dA 377 -35.81 -8.44 2.30e+01 1gw5B 591 -41.55 -8.39 2.36e+01 1pzlA 237 -31.31 -8.33 2.43e+01 1j1jA 240 -35.31 -8.28 2.49e+01 1br2A 791 -30.59 -8.24 2.55e+01 1clqA 903 -40.76 -8.22 2.58e+01 1jsqA 582 -41.44 -8.18 2.64e+01 1b9zA 516 -28.68 -8.17 2.65e+01 1f8mA 429 -24.95 -8.14 2.68e+01 1mtyG 162 -24.65 -8.14 2.69e+01 1be3C 379 -52.48 -8.12 2.72e+01 1h16A 759 -34.44 -7.94 2.99e+01 1oaoA 674 -37.09 -7.91 3.03e+01 1jcrA 377 -36.19 -7.89 3.08e+01 1ujnA 348 -25.76 -7.85 3.13e+01 3pflA 759 -33.38 -7.80 3.21e+01 1f4tA 368 -29.86 -7.80 3.22e+01 1a76 326 -25.38 -7.66 3.47e+01 1wmdA 434 -22.41 -7.62 3.54e+01 1f88A 348 -50.45 -7.61 3.57e+01 1ls6A 295 -22.54 -7.60 3.59e+01 1fhjB 146 -25.59 -7.55 3.68e+01 1e8xA 961 -41.44 -7.54 3.69e+01 1ih7A 903 -39.67 -7.53 3.73e+01 5bcaA 516 -27.42 -7.51 3.75e+01 1qbqA 333 -34.86 -7.50 3.77e+01 1nvmA 345 -22.02 -7.48 3.83e+01 1mmoG 162 -23.70 -7.47 3.85e+01 1lrv 244 -22.60 -7.40 3.99e+01